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Sodium in PDB 7ae7: Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X)

Enzymatic activity of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X)

All present enzymatic activity of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X):
4.1.1.61; 4.1.1.63;

Protein crystallography data

The structure of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X), PDB code: 7ae7 was solved by S.A.Marshall, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.42 / 2.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.553, 200.945, 201.991, 90, 90, 90
R / Rfree (%) 18 / 22.7

Other elements in 7ae7:

The structure of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X) also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X) (pdb code 7ae7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X), PDB code: 7ae7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7ae7

Go back to Sodium Binding Sites List in 7ae7
Sodium binding site 1 out of 5 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:49.4
occ:1.00
 OD1 A:ASP413 2.3 44.5 1.0
O A:HOH714 2.4 39.7 1.0
OD1 C:ASN419 2.5 73.4 1.0
OD2 A:ASP441 2.8 53.7 1.0
CG A:ASP413 3.3 27.7 1.0
OE2 A:GLU449 3.4 62.7 1.0
O A:HOH630 3.5 27.6 1.0
CG C:ASN419 3.6 75.3 1.0
CG A:ASP441 3.7 35.1 1.0
OD2 A:ASP413 3.8 30.7 1.0
OE1 A:GLU449 3.8 62.8 1.0
CD A:GLU449 4.1 62.9 1.0
ND2 C:ASN419 4.1 68.5 1.0
O A:HOH608 4.4 38.8 1.0
CB A:ASP413 4.4 18.6 1.0
OD1 A:ASP441 4.4 27.0 1.0
O A:THR443 4.6 28.0 1.0
O A:ASP441 4.6 22.1 1.0
CB A:ASP441 4.6 20.7 1.0
CB C:ASN419 4.7 58.6 1.0
CA A:ASP413 4.8 21.7 1.0

Sodium binding site 2 out of 5 in 7ae7

Go back to Sodium Binding Sites List in 7ae7
Sodium binding site 2 out of 5 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:28.0
occ:1.00
 OD1 B:ASP413 2.3 36.3 1.0
O B:HOH640 2.3 42.6 1.0
O B:HOH607 2.4 33.7 1.0
OD2 B:ASP441 2.4 32.0 1.0
ND2 E:ASN419 2.4 35.2 1.0
CG B:ASP413 3.0 32.1 1.0
OD2 B:ASP413 3.2 28.0 1.0
CG E:ASN419 3.2 39.6 1.0
OD1 E:ASN419 3.5 45.3 1.0
CG B:ASP441 3.5 30.3 1.0
OE2 B:GLU449 3.7 44.8 1.0
O B:HOH637 3.9 25.5 1.0
O E:HOH611 4.0 26.6 1.0
OE1 B:GLU449 4.0 44.2 1.0
CD B:GLU449 4.3 43.4 1.0
OD1 B:ASP441 4.3 19.2 1.0
CB B:ASP441 4.3 19.0 1.0
CB B:ASP413 4.4 18.5 1.0
O B:HOH603 4.4 26.3 1.0
CB E:ASN419 4.5 30.8 1.0
O B:THR443 4.5 20.5 1.0
O B:HOH623 4.7 28.1 1.0
O B:ASP441 4.8 21.2 1.0
CA B:ASP413 4.9 23.0 1.0

Sodium binding site 3 out of 5 in 7ae7

Go back to Sodium Binding Sites List in 7ae7
Sodium binding site 3 out of 5 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:31.6
occ:1.00
 OD1 C:ASP413 2.4 31.1 1.0
O C:HOH616 2.4 36.4 1.0
ND2 A:ASN419 2.4 38.0 1.0
O C:HOH618 2.5 23.3 1.0
OD2 C:ASP441 2.8 35.3 1.0
OE2 C:GLU449 2.9 44.8 1.0
CG A:ASN419 3.1 33.5 1.0
OD1 A:ASN419 3.1 30.0 1.0
CG C:ASP413 3.3 32.5 1.0
OE1 C:GLU449 3.4 46.2 1.0
CD C:GLU449 3.5 44.9 1.0
OD2 C:ASP413 3.6 28.8 1.0
CG C:ASP441 4.0 31.8 1.0
CB A:ASN419 4.4 29.2 1.0
O C:HOH641 4.7 37.9 1.0
CB C:ASP413 4.7 24.4 1.0
O C:THR443 4.8 28.0 1.0
OD1 C:ASP441 4.8 27.5 1.0
CB C:ASP441 4.8 27.9 1.0
O C:HOH603 4.9 28.6 1.0

Sodium binding site 4 out of 5 in 7ae7

Go back to Sodium Binding Sites List in 7ae7
Sodium binding site 4 out of 5 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na501

b:41.8
occ:1.00
 O E:HOH633 2.5 37.2 1.0
ND2 B:ASN419 2.5 47.3 1.0
OD2 E:ASP441 2.8 47.7 1.0
OD1 E:ASP413 2.9 34.1 1.0
OE2 E:GLU449 3.0 57.3 1.0
OE1 E:GLU449 3.2 48.6 1.0
CD E:GLU449 3.5 56.8 1.0
CG B:ASN419 3.6 58.0 1.0
CG E:ASP441 3.7 32.7 1.0
OD1 B:ASN419 3.8 49.2 1.0
CG E:ASP413 3.8 34.6 1.0
OD2 E:ASP413 4.0 36.9 1.0
O E:THR443 4.1 33.2 1.0
OD1 E:ASP441 4.2 32.5 1.0
O E:HOH603 4.3 36.5 1.0
O E:HOH601 4.4 36.2 1.0
OG1 E:THR443 4.5 33.3 1.0
CG E:PRO445 4.7 40.8 1.0
CB E:ASP441 4.7 23.8 1.0
CA E:PRO445 4.9 38.0 1.0
CB B:ASN419 4.9 44.1 1.0
N E:PRO445 4.9 31.5 1.0
O E:ASP441 5.0 23.7 1.0
CD E:PRO445 5.0 43.0 1.0

Sodium binding site 5 out of 5 in 7ae7

Go back to Sodium Binding Sites List in 7ae7
Sodium binding site 5 out of 5 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, with Truncated Shvdcd (V59X) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na501

b:43.7
occ:1.00
 OD1 F:ASP413 2.3 35.0 1.0
O F:HOH632 2.4 42.6 1.0
OD1 D:ASN419 2.5 40.1 1.0
OD2 F:ASP441 2.6 44.1 1.0
CG F:ASP413 3.0 32.9 1.0
OE2 F:GLU449 3.0 48.8 1.0
OD2 F:ASP413 3.0 35.8 1.0
CG D:ASN419 3.5 40.8 1.0
CG F:ASP441 3.6 37.8 1.0
CD F:GLU449 3.9 48.1 1.0
ND2 D:ASN419 3.9 45.6 1.0
OE1 F:GLU449 3.9 52.1 1.0
O F:HOH610 4.3 33.2 1.0
O F:THR443 4.3 39.2 1.0
OD1 F:ASP441 4.4 35.5 1.0
CB F:ASP413 4.4 24.7 1.0
CB F:ASP441 4.5 25.4 1.0
O F:ASP441 4.6 24.3 1.0
CB D:ASN419 4.7 35.5 1.0
O F:HOH606 4.9 31.7 1.0

Reference:

S.A.Marshall, K.A.P.Payne, D.Leys. Domain Mobility and Allosteric Activation of Ubid Decarboxylases To Be Published.
Page generated: Tue Oct 8 15:52:55 2024

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